Predefined list of transformation functions for count data normalization.
Format
A named list of transformation functions:
- none
Identity transformation (no change)
- sqrt
Square root transformation
- log2
log2(x+1) transformation
- vst
Variance stabilizing transformation (DESeq2)
- rlog
Regularized log transformation (DESeq2)
- rank
Rank transformation within each sample
Details
This object provides a list of predefined transformation functions for gene expression matrix. For `rlog()` and `vst()` transformations (from `DESeq2`), the expression matrix is multiplied by 2 prior to rounding. This is done to preserve more information for the lower expression values (especially for TPM).